The National Library of Medicine continues its Visible Human project with the Visible Woman. This paper describes on-going results in processing the CT data using the methodology described in Marching Through The Visible Man.
Make Your Own Visible Woman shows how to use the Visualization Toolkit to make and render surface models of the Visible Woman.
For more examples of 3D medical imaging done in our laboratory go to our Scientific Movie Library.
On a Unix system, these files can be converted into files without headers with the following script:
#!/bin/csh set n = 1001 set m = 1 while ($n <= 2734) zcat c_vf$n.fre.Z | dd ibs=3416 skip=1 | compress - >slice.$m.Z @ n = $n + 1 @ m = $m + 1 end
The first step to understand the data was to print the header information. In particular, we need to know the size of the pixels, and the distance between each slice.
The fresh CT data was acquired in several sections with varying pixel
The following table summarizes the data.
|Summary of the Fresh CT Data|
|Section||Slice Range||FOV||Pixel Size||Spacing|
This work was done on an Onyx Reality Engine 2 (Silicon Graphics, Mountain View, CA) with the following configuration:
2 150 MHZ IP19 Processors CPU: MIPS R4400 Processor Chip Revision: 5.0 FPU: MIPS R4010 Floating Point Chip Revision: 0.0 Data cache size: 16 Kbytes Instruction cache size: 16 Kbytes Secondary unified instruction/data cache size: 1 Mbyte Main memory size: 256 Mbytes, 2-way interleaved RealityEngineII Graphics Pipe 0 at IO Slot 3 Physical Adapter 2 (Fchip rev 2)
The Reality Engine was running Irix 5.3. We used a variety of software tools we call the Research Workstation all developed in-house. All of the software works with 16-bit medical images. These are described in the Visible Man companion to this paper. We did apply one new operation to the data after decimation. We smoothed the decimated triangle vertices with a Laplacian smoothing algorithm.
The following table contains triangle counts and timings for each of sections.
|Summary of Visible Woman Surface Extraction|
|Section||Slice Range||Skin Original Tri's||Marching Time (sec)||Skin Decimated Tri's||Decimate Smooth Time (sec)||Bone Original Tri's||Marching Time (sec)||Bone Decimated Tri's||Decimate Smooth Time (sec)|
We continued by reconstructing the entire skin and bone model. We used seeds to selected connected components before applying the Marching Cubes algorithm. We also split sections 3 and 6 into smaller pieces to reduce memory requirements during model decimation and smoothing.
|Full Body Surface Models|
Some full body models:
A little java.
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